There is a v2 to v3 migration guide here : https://learn.microsoft.com/en-us/azure/media-services/latest/migrate-v-2-v-3-migration-introduction
From what I understand, you are using AMS v2 only for key/license delivery, not for packaging/streaming, right ?
This scenario is not recommended with AMS v3. I think the main reason is because content protection in v3 relies the streaming locator object (related to an asset). In your case, you don't have AMS assets....